Stephen Pickles

The Application Hosting Environment: Lightweight Middleware for Grid-Based Computational Science

Abstract Grid computing is distributed computing performed transparently across multiple administrative domains. Grid middleware, which is meant to enable access to grid resources, is currently widely seen as being too heavyweight and, in consequence, unwieldy for general scientific use. Its heavyweight nature, especially on the client-side, has severely restricted the uptake of grid technology by computational scientists. In this paper, we describe the Application Hosting Environment (AHE) which we have developed to address some of these problems. The AHE is a lightweight, easily deployable environment designed to allow the scientist to quickly and easily run legacy applications on distributed grid resources. It provides a higher level abstraction of a grid than is offered by existing grid middleware schemes such as the Globus Toolkit. As a result, the computational scientist does not need to know the details of any particular underlying grid middleware and is isolated from any changes to it on the distributed resources. The functionality provided by the AHE is ‘application-centric’: applications are exposed as web services with a well-defined standards-compliant interface. This allows the computational scientist to start and manage application instances on a grid in a transparent manner, thus greatly simplifying the user experience. We describe how a range of computational science codes have been hosted within the AHE and how the design of the AHE allows us to implement complex workflows for deployment on grid infrastructure.

Steering in computational science: mesoscale modelling and simulation

This paper outlines the benefits of computational steering for high performance computing applications. Lattice-Boltzmann mesoscale fluid simulations of binary and ternary amphiphilic fluids in two and three dimensions are used to illustrate the substantial improvements which computational steering offers in terms of resource efficiency and time to discover new physics. We discuss details of our current steering implementations and describe their future outlook with the advent of computational grids.

Instability in the molecular dynamics step of a hybrid Monte Carlo algorithm in dynamical fermion lattice QCD simulations

We investigate instability and reversibility within hybrid Monte Carlo simulations using a nonperturbatively improved Wilson action. We demonstrate the onset of instability as tolerance parameters and molecular dynamics step sizes are varied. We compare these findings with theoretical expectations and present limits on simulation parameters within which a stable and reversible algorithm is obtained for physically relevant simulations. Results of optimization experiments with respect to tolerance parameters are also presented.

Large scale computational science on federated international grids: The role of switched optical networks

The provision of high performance compute and data resources on a grid has often been the primary concern of grid resource providers, with the network links used to connect them only a secondary matter. Certain large scale distributed scientific simulations, especially ones which involve cross-site runs or interactive visualisation and steering capabilities, often require high quality of service, high bandwidth, low latency network interconnects between resources. In this paper, we describe three applications which require access to such network infrastructure, together with the middleware and policies needed to make them possible.

The TeraGyroid experiment -- Supercomputing 2003

Amphiphiles are molecules with hydrophobic tails and hydrophilic heads. When dispersed in solvents, they self assemble into complex mesophases including the beautiful cubic gyroid phase. The goal of the TeraGyroid experiment was to study defect pathways and dynamics in these gyroids. The UKs supercomputing and USAs TeraGrid facilities were coupled together, through a dedicated high-speed network, into a single computational Grid for research work that peaked around the Supercomputing 2003 conference. The gyroids were modeled using lattice Boltzmann methods with parameter spaces explored using many 128^{3} and 256^{3} grid point simulations, this data being used to inform the worlds largest three-dimensional time dependent simulation with 1024^{3}-grid points. The experiment generated some 2 TBytes of useful data. In terms of Grid technology the project demonstrated the migration of simulations (using Globus middleware) to and fro across the Atlantic exploiting the availability of resources. Integration of the systems accelerated the time to insight. Distributed visualisation of the output datasets enabled the parameter space of the interactions within the complex fluid to be explored from a number of sites, informed by discourse over the Access Grid. The project was sponsored by EPSRC (UK) and NSF (USA) with trans-Atlantic optical bandwidth provided by British Telecommunications.

Parallel tempering in lattice QCD with O(a)-improved Wilson fermions

We present details of our investigations of the parallel tempering algorithm. We consider the application of action matching technology to the selection of parameters. We then present a simple model of the autocorrelations for a particular parallel tempered system. Finally we present results from applying the algorithm to lattice QCD with O(a)-improved dynamical Wilson fermions for twin sub-ensemble systems. (S0556-2821(99)08109-6)

Coupled applications on distributed resources

Coupled models are set to become increasingly important in all aspects of science and engineering as tools with which to study complex systems in an integrated manner. Such coupled, hybrid simulations typically communicate data between the component models of which they are comprised relatively infrequently, and so a Grid is expected to present an ideal architecture on which to run them. In the present paper, we describe a simple, flexible and extensible architecture for a two-component hybrid molecular-continuum coupled model (hybrid MD). We discuss its deployment on distributed resources and the extensions to the RealityGrid computational-steering system to handle coupled models.

Workflows in Pulsar Astronomy

In this chapter, we describe the development of methods that operate on the output of the signal of a radio telescope to detect the characteristic signals of pulsars. These signals are much weaker than the noise in the signal at any given wavelength, and therefore algorithms for combining the signals in different wavelength bands must be applied. This is heavily expensive in terms of CPU power. Early versions of distributed algorithms ran on a distributed network of supercomputers connected by Internet-aware Message Passing Interface (MPI) during the period 1999–2001. Today such techniques are being integrated into workflows that automate the search process and enable sophisticated astronomical knowledge to be captured via the construction of the workflow. In particular, we address issues of parallelism within components of the workflow. Parallelism is necessary due to two constraints on workflow performance. One is the application of the workflow in real time as the signal is being processed to enable very precise measurements to be carried out on known pulsars. The other is the use of the workflow to explore large regions of parameter space in search of previously undetected pulsars. There are very severe restraints on the degree of abstraction that can currently be applied in this work since details of the architecture of the computing resource (parallel cluster or computational Grid) on which the workflows are to be run cannot be ignored in the construction of the workflow.

GRENADE: a Grid Enabled Desktop Environment

Making grid technology available to a wider community requires moving away from the complex command line tools commonly in use today towards a more transparent and user-friendly interface. We seek to address this challenge by presenting the notion of a Grid Enabled Desktop Environment (GRENADE), seamlessly extending the familiar desktop user-interface paradigm to interactions with grid resources. This paper describes our initial implementation.